Designing multifunctional agroecosystems that provide a diverse suite of ecosystem services is essential to human well-being. Among the most indispensable agroecosystem services are those related to nitrogen (N), an essential nutrient for crop growth that has become one of the most pervasive pollutants of our time. Applying ecological principles to manage N is a viable strategy to optimize agricultural N cycling. The goals of this dissertation research were to: (1) identify key drivers of N dynamics in systems using ecologically-based nutrient management (ENM) and (2) determine if and how aboveground diversity in ENM supports N-related and other ecosystem services. Using data from a five year study of four organic cropping systems, I employed recursive partitioning models to pinpoint management and environment factors that drive soil inorganic N (SIN) dynamics in ENM and identify conditions under which elevated SIN leads to N leaching loss. I found that social factors from farmer decisions to national policies shape the extent to which ENM can effectively promote multiple N-related services and identified tillage as a key leverage point that shapes N cycling in ENM. In a two year field study of cover crop systems ranging in diversity from one to eight species, I focused my investigation of ENM on the impacts of aboveground diversity (an ecological principle frequently applied in ENM) on five ecosystem services. This research showed that just as aboveground diversity enhances ecosystem function in natural systems, cover crop diversity enhances ecosystem services in agroecosystems. This experiment also tested several paths by which cover crop diversity impacts N retention, N provision, N supply, weed suppression, subsequent crop yield, and multifunctionality. Aboveground, individual ecosystem services were correlated with cover crop productivity and the carbon:nitrogen ratio of cover crop biomass. Belowground, cover crops exerted species-specific influences on microbial community structure and increasing cover crop diversity was positively correlated with microbial functional diversity, two linkages that may impact ecosystem services from diverse mixtures. Using an array of diversity indices, I also found direct effects of cover crop diversity on ecosystem services, and concluded that achieving multifunctionality with cover crops requires not only increased species richness, but also functional diversity.